From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Sat, 19 Feb 2011 18:53:30 +0000 (+0000)
Subject: added qual clipping to ruby code
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=01be4549a8a7b9ac9d9e543b3a147d5270c8e68a;p=biopieces.git

added qual clipping to ruby code

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1276 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/Maasha/lib/seq.rb
index 72ca1cd..de13ec2 100644
--- a/code_ruby/Maasha/lib/seq.rb
+++ b/code_ruby/Maasha/lib/seq.rb
@@ -336,7 +336,8 @@ class Seq
     pos = self.adaptor_locate_right(adaptor)
 
     if pos > 0
-      self.seq = self.seq[0 ... pos]
+      self.seq  = self.seq[0 ... pos]
+      self.qual = self.qual[0 ... pos] unless self.qual.nil?
     end
   end
 
@@ -347,7 +348,8 @@ class Seq
     pos = self.adaptor_locate_left(adaptor)
 
     if pos > 0
-      self.seq = self.seq[pos + 1 ... self.seq.length]
+      self.seq  = self.seq[pos + 1 ... self.seq.length]
+      self.qual = self.qual[pos + 1 ... self.qual.length] unless self.qual.nil?
     end
   end
 
diff --git a/code_ruby/Maasha/test/test_seq.rb b/code_ruby/Maasha/test/test_seq.rb
index 8668738..2482422 100755
--- a/code_ruby/Maasha/test/test_seq.rb
+++ b/code_ruby/Maasha/test/test_seq.rb
@@ -290,12 +290,26 @@ class TestSeq < Test::Unit::TestCase
     assert_equal( "nnnnn", @entry.seq)
   end
 
+  def test_Seq_adaptor_clip_right_returns_correct_qual
+    @entry.seq  = "nnnnncgat"
+    @entry.qual = "abcdefghi"
+    @entry.adaptor_clip_right("cgat")
+    assert_equal( "abcde", @entry.qual)
+  end
+
   def test_Seq_adaptor_clip_left_returns_correct_sequence
     @entry.seq = "cgatnnnnn"
     @entry.adaptor_clip_left("cgat")
     assert_equal( "nnnnn", @entry.seq)
   end
 
+  def test_Seq_adaptor_clip_left_returns_correct_qual
+    @entry.seq  = "cgatnnnnn"
+    @entry.qual = "abcdefghi"
+    @entry.adaptor_clip_left("cgat")
+    assert_equal( "efghi", @entry.qual)
+  end
+
   def test_Digest_new_raises_on_bad_pattern_residue
     assert_raise(DigestError) { Digest.new(@entry, "X", 4) }
   end